Correlation between copy number variations of arm-level result and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1125S48

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 81 arm-level events and 10 molecular subtypes across 441 patients, 426 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
3p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
4p gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
4q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q gain cnv correlated to 'CN_CNMF'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
8p gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
8q gain cnv correlated to 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
11p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
12q gain cnv correlated to 'RPPA_CNMF'.
13q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
14q gain cnv correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CHIERARCHICAL'.
16q gain cnv correlated to 'CN_CNMF'.
17p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19p gain cnv correlated to 'CN_CNMF' and 'RPPA_CNMF'.
19q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q gain cnv correlated to 'CN_CNMF'.
xp gain cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.
xq gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
3p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
6q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
8p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
8q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
13q loss cnv correlated to 'CN_CNMF'.
14q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
21q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xp loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 426 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
8p loss	91 (21%)	350	1e-05 (5.91e-05)	0.0005 (0.0018)	0.0373 (0.0745)	0.035 (0.0712)	0.00023 (0.000891)	0.00018 (0.000711)	0.0142 (0.0323)	0.00132 (0.00411)	0.00735 (0.0185)	0.0001 (0.000429)
17p loss	164 (37%)	277	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0107 (0.0254)	0.00311 (0.00859)	1e-05 (5.91e-05)	3e-05 (0.000151)	0.00044 (0.00161)	1e-05 (5.91e-05)	0.0356 (0.0721)	0.00016 (0.000648)
11q gain	74 (17%)	367	1e-05 (5.91e-05)	8e-05 (0.000364)	0.0366 (0.0734)	0.191 (0.273)	0.0208 (0.0455)	0.00678 (0.0173)	5e-05 (0.000238)	6e-05 (0.000281)	0.0176 (0.0391)	7e-05 (0.000324)
18p gain	85 (19%)	356	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.455 (0.549)	0.00061 (0.00212)	0.0001 (0.000429)	0.0431 (0.0836)	0.00027 (0.00104)	5e-05 (0.000238)	0.00032 (0.0012)	0.00324 (0.00887)
9q loss	104 (24%)	337	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.824 (0.868)	0.00337 (0.00913)	1e-05 (5.91e-05)	0.00111 (0.00358)	3e-05 (0.000151)	1e-05 (5.91e-05)	0.0359 (0.0725)	4e-05 (0.000194)
18q loss	154 (35%)	287	1e-05 (5.91e-05)	2e-05 (0.000107)	0.854 (0.888)	0.0375 (0.0747)	0.0033 (0.009)	0.00018 (0.000711)	0.0264 (0.0556)	0.00124 (0.00395)	0.0348 (0.0711)	0.00015 (0.000614)
19p loss	116 (26%)	325	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.363 (0.463)	0.00367 (0.00988)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.00097 (0.00319)	1e-05 (5.91e-05)
6q gain	66 (15%)	375	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0384 (0.0754)	0.0655 (0.116)	1e-05 (5.91e-05)	0.0203 (0.0446)	3e-05 (0.000151)	0.00018 (0.000711)	0.077 (0.132)	3e-05 (0.000151)
20p gain	242 (55%)	199	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0625 (0.112)	0.0186 (0.0413)	2e-05 (0.000107)	2e-05 (0.000107)	4e-05 (0.000194)	1e-05 (5.91e-05)	0.0878 (0.148)	8e-05 (0.000364)
20q gain	280 (63%)	161	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0884 (0.148)	0.00143 (0.00439)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0624 (0.112)	1e-05 (5.91e-05)
9p loss	149 (34%)	292	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.493 (0.586)	6e-05 (0.000281)	1e-05 (5.91e-05)	0.00012 (0.000501)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0667 (0.117)	0.00011 (0.000464)
12p loss	62 (14%)	379	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.339 (0.439)	0.335 (0.435)	1e-05 (5.91e-05)	0.00014 (0.000576)	0.00113 (0.00363)	1e-05 (5.91e-05)	0.0091 (0.0221)	1e-05 (5.91e-05)
14q loss	111 (25%)	330	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.748 (0.811)	0.251 (0.338)	0.00013 (0.000537)	0.00129 (0.00408)	0.00031 (0.00117)	3e-05 (0.000151)	0.0318 (0.0655)	0.0103 (0.0246)
15q loss	90 (20%)	351	1e-05 (5.91e-05)	0.0003 (0.00114)	0.017 (0.038)	0.433 (0.53)	0.0001 (0.000429)	0.00103 (0.00338)	0.046 (0.0887)	0.00445 (0.0118)	0.246 (0.334)	0.00094 (0.00311)
16p loss	100 (23%)	341	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.359 (0.459)	0.375 (0.476)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.00104 (0.0034)	1e-05 (5.91e-05)
16q loss	114 (26%)	327	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.919 (0.936)	0.0578 (0.105)	1e-05 (5.91e-05)	0.00011 (0.000464)	2e-05 (0.000107)	1e-05 (5.91e-05)	0.00249 (0.0071)	3e-05 (0.000151)
19q loss	86 (20%)	355	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.698 (0.767)	0.063 (0.112)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.00636 (0.0163)	1e-05 (5.91e-05)
21q loss	181 (41%)	260	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.201 (0.284)	0.32 (0.416)	0.0011 (0.00356)	0.00312 (0.00859)	0.0259 (0.0546)	0.00056 (0.00199)	0.0119 (0.0275)	0.00044 (0.00161)
22q loss	146 (33%)	295	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.873 (0.9)	0.00212 (0.00618)	0.00199 (0.00588)	0.00771 (0.0192)	3e-05 (0.000151)	1e-05 (5.91e-05)	0.0917 (0.153)	0.00065 (0.00223)
1p gain	50 (11%)	391	1e-05 (5.91e-05)	0.00552 (0.0143)	0.105 (0.17)	0.105 (0.17)	0.00045 (0.00163)	0.0783 (0.134)	0.00041 (0.00151)	0.00194 (0.00576)	0.00147 (0.00448)	0.00797 (0.0197)
1q gain	105 (24%)	336	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.125 (0.196)	0.0161 (0.0362)	9e-05 (0.000401)	0.081 (0.138)	1e-05 (5.91e-05)	0.00062 (0.00215)	0.053 (0.0989)	0.00313 (0.00859)
5p gain	100 (23%)	341	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.786 (0.845)	0.111 (0.177)	2e-05 (0.000107)	0.00059 (0.00208)	0.00067 (0.00228)	1e-05 (5.91e-05)	0.0865 (0.146)	0.00029 (0.00111)
6p gain	81 (18%)	360	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.06 (0.109)	0.0519 (0.0978)	1e-05 (5.91e-05)	0.00474 (0.0124)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.231 (0.318)	4e-05 (0.000194)
13q gain	153 (35%)	288	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0757 (0.131)	0.865 (0.896)	2e-05 (0.000107)	0.00384 (0.0103)	1e-05 (5.91e-05)	0.00059 (0.00208)	0.564 (0.643)	0.00397 (0.0106)
1p loss	58 (13%)	383	1e-05 (5.91e-05)	9e-05 (0.000401)	0.732 (0.796)	0.51 (0.599)	0.00135 (0.00417)	0.00309 (0.00859)	0.00469 (0.0123)	0.00689 (0.0175)	0.304 (0.398)	0.00489 (0.0127)
3p loss	93 (21%)	348	1e-05 (5.91e-05)	0.00019 (0.000747)	0.612 (0.689)	0.457 (0.55)	2e-05 (0.000107)	0.00311 (0.00859)	0.0417 (0.0814)	0.00084 (0.0028)	0.0863 (0.146)	0.00131 (0.0041)
3q loss	56 (13%)	385	1e-05 (5.91e-05)	0.0001 (0.000429)	0.0654 (0.116)	0.343 (0.444)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.00146 (0.00446)	0.0108 (0.0255)	0.163 (0.241)	7e-05 (0.000324)
4p loss	167 (38%)	274	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.498 (0.589)	0.305 (0.398)	1e-05 (5.91e-05)	0.0703 (0.123)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.00977 (0.0235)	1e-05 (5.91e-05)
4q loss	165 (37%)	276	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.893 (0.915)	0.0521 (0.0978)	2e-05 (0.000107)	0.0259 (0.0546)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.186 (0.268)	2e-05 (0.000107)
5p loss	63 (14%)	378	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.969 (0.976)	0.48 (0.573)	1e-05 (5.91e-05)	0.00061 (0.00212)	2e-05 (0.000107)	1e-05 (5.91e-05)	0.148 (0.225)	4e-05 (0.000194)
5q loss	108 (24%)	333	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.756 (0.818)	0.291 (0.384)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.0575 (0.105)	1e-05 (5.91e-05)
10q loss	68 (15%)	373	1e-05 (5.91e-05)	2e-05 (0.000107)	0.686 (0.757)	0.0552 (0.102)	3e-05 (0.000151)	0.00192 (0.00572)	0.00268 (0.00759)	2e-05 (0.000107)	0.139 (0.215)	0.0235 (0.0507)
11p loss	64 (15%)	377	1e-05 (5.91e-05)	5e-05 (0.000238)	0.0654 (0.116)	0.0201 (0.0444)	0.0124 (0.0284)	0.0215 (0.0468)	0.196 (0.279)	0.00694 (0.0176)	0.063 (0.112)	0.00209 (0.00613)
17q loss	74 (17%)	367	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.771 (0.833)	0.0665 (0.117)	4e-05 (0.000194)	0.0249 (0.0531)	0.00161 (0.00485)	1e-05 (5.91e-05)	0.436 (0.532)	0.0308 (0.0637)
2p gain	78 (18%)	363	1e-05 (5.91e-05)	2e-05 (0.000107)	0.453 (0.547)	0.529 (0.616)	0.0117 (0.0273)	0.156 (0.234)	0.00819 (0.0202)	0.00094 (0.00311)	0.097 (0.16)	0.0254 (0.0539)
7p gain	202 (46%)	239	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.537 (0.621)	0.14 (0.215)	0.00773 (0.0192)	0.0427 (0.0831)	0.146 (0.222)	0.011 (0.0258)	0.0951 (0.158)	0.00817 (0.0202)
15q gain	39 (9%)	402	1e-05 (5.91e-05)	0.00204 (0.00601)	0.359 (0.459)	0.0528 (0.0988)	0.0233 (0.0503)	0.0376 (0.0747)	0.0631 (0.112)	0.00313 (0.00859)	0.224 (0.31)	0.00623 (0.016)
19q gain	79 (18%)	362	1e-05 (5.91e-05)	0.104 (0.169)	0.0109 (0.0258)	0.0237 (0.0509)	0.137 (0.212)	0.0955 (0.158)	0.0432 (0.0836)	0.0681 (0.12)	0.0377 (0.0747)	0.00885 (0.0217)
21q gain	22 (5%)	419	0.00053 (0.0019)	0.00448 (0.0119)	0.106 (0.172)	0.467 (0.561)	0.00021 (0.000818)	0.244 (0.332)	0.0276 (0.058)	0.00056 (0.00199)	0.679 (0.754)	0.00237 (0.00683)
6p loss	50 (11%)	391	1e-05 (5.91e-05)	9e-05 (0.000401)	0.0122 (0.0281)	0.514 (0.601)	0.00221 (0.00642)	0.0304 (0.0633)	0.515 (0.601)	0.011 (0.0258)	0.0962 (0.159)	0.203 (0.287)
7p loss	17 (4%)	424	0.00065 (0.00223)	0.00174 (0.0052)	0.246 (0.334)	0.961 (0.971)	0.00228 (0.0066)	0.643 (0.72)	0.00075 (0.00253)	0.00428 (0.0114)	0.0542 (0.101)	0.0366 (0.0734)
10p loss	64 (15%)	377	1e-05 (5.91e-05)	0.0012 (0.00384)	0.481 (0.573)	0.0775 (0.133)	0.00166 (0.00498)	0.00135 (0.00417)	0.00108 (0.00351)	0.00031 (0.00117)	0.0904 (0.151)	0.164 (0.241)
12q loss	52 (12%)	389	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.688 (0.758)	0.58 (0.66)	0.0001 (0.000429)	0.00293 (0.00821)	0.0967 (0.159)	0.0001 (0.000429)	0.0577 (0.105)	0.00067 (0.00228)
2q gain	66 (15%)	375	2e-05 (0.000107)	0.00072 (0.00244)	0.499 (0.59)	0.558 (0.638)	0.0021 (0.00614)	0.0755 (0.131)	0.00751 (0.0188)	0.00898 (0.0219)	0.737 (0.8)	0.237 (0.324)
10p gain	98 (22%)	343	1e-05 (5.91e-05)	1e-05 (5.91e-05)	0.806 (0.86)	0.392 (0.49)	0.0074 (0.0186)	0.125 (0.196)	0.0506 (0.0958)	0.00061 (0.00212)	0.545 (0.628)	0.016 (0.0362)
11p gain	62 (14%)	379	1e-05 (5.91e-05)	0.00011 (0.000464)	0.255 (0.342)	0.291 (0.384)	0.0578 (0.105)	0.0858 (0.145)	0.00021 (0.000818)	0.00026 (0.001)	0.0693 (0.121)	0.00965 (0.0234)
17q gain	64 (15%)	377	1e-05 (5.91e-05)	0.0008 (0.00269)	0.863 (0.895)	0.555 (0.636)	0.00048 (0.00174)	0.00529 (0.0137)	0.207 (0.291)	0.383 (0.482)	0.159 (0.237)	0.0219 (0.0476)
6q loss	69 (16%)	372	1e-05 (5.91e-05)	0.0001 (0.000429)	0.0971 (0.16)	0.678 (0.753)	0.00083 (0.00278)	0.0047 (0.0123)	0.508 (0.598)	0.0356 (0.0721)	0.113 (0.179)	0.287 (0.38)
7q loss	29 (7%)	412	1e-05 (5.91e-05)	0.00033 (0.00123)	0.153 (0.231)	0.824 (0.868)	8e-05 (0.000364)	0.417 (0.515)	0.00013 (0.000537)	0.00251 (0.00713)	0.113 (0.179)	0.14 (0.215)
3q gain	91 (21%)	350	0.00018 (0.000711)	0.0121 (0.0279)	0.0514 (0.0971)	0.22 (0.307)	0.296 (0.389)	0.021 (0.046)	0.0168 (0.0375)	0.0791 (0.135)	0.134 (0.208)	0.0769 (0.132)
18q gain	55 (12%)	386	0.038 (0.0749)	0.0118 (0.0275)	0.821 (0.868)	0.0521 (0.0978)	0.0137 (0.0312)	0.381 (0.481)	0.0532 (0.099)	0.0151 (0.0342)	0.114 (0.181)	0.173 (0.254)
xq gain	55 (12%)	386	0.032 (0.0658)	0.0306 (0.0637)	0.975 (0.981)	0.809 (0.861)	0.177 (0.258)	0.0224 (0.0486)	0.0367 (0.0734)	0.453 (0.547)	0.827 (0.869)	0.228 (0.316)
1q loss	25 (6%)	416	9e-05 (0.000401)	0.00012 (0.000501)	0.846 (0.881)	0.537 (0.621)	0.0716 (0.125)	0.0103 (0.0246)	0.344 (0.445)	0.0904 (0.151)	0.426 (0.524)	0.00142 (0.00437)
2p loss	23 (5%)	418	0.00016 (0.000648)	6e-05 (0.000281)	0.162 (0.24)	0.198 (0.281)	0.0308 (0.0637)	0.599 (0.678)	0.157 (0.235)	0.146 (0.222)	0.0473 (0.0909)	0.659 (0.736)
8q loss	37 (8%)	404	1e-05 (5.91e-05)	0.431 (0.528)	0.384 (0.482)	0.431 (0.528)	0.0176 (0.0391)	0.0611 (0.11)	0.0203 (0.0446)	0.145 (0.222)	0.838 (0.873)	0.0434 (0.0839)
xq loss	55 (12%)	386	1e-05 (5.91e-05)	3e-05 (0.000151)	0.965 (0.973)	0.0479 (0.0916)	0.0924 (0.154)	0.0851 (0.145)	0.404 (0.504)	0.0476 (0.0912)	0.057 (0.105)	0.212 (0.297)
8q gain	240 (54%)	201	0.41 (0.509)	4e-05 (0.000194)	0.426 (0.524)	0.512 (0.599)	0.154 (0.232)	0.985 (0.99)	0.0131 (0.03)	0.0348 (0.0711)	0.188 (0.271)	0.0597 (0.108)
16p gain	58 (13%)	383	0.0046 (0.0121)	0.049 (0.0932)	0.453 (0.547)	0.0114 (0.0268)	0.452 (0.547)	0.189 (0.272)	0.763 (0.825)	0.715 (0.782)	0.821 (0.868)	0.141 (0.217)
17p gain	29 (7%)	412	0.00271 (0.00762)	0.0084 (0.0206)	0.898 (0.918)	0.948 (0.96)	0.107 (0.172)	0.22 (0.307)	0.231 (0.318)	0.476 (0.568)	0.108 (0.173)	0.0249 (0.0531)
2q loss	30 (7%)	411	1e-05 (5.91e-05)	0.00018 (0.000711)	0.381 (0.481)	0.349 (0.449)	0.144 (0.22)	0.648 (0.724)	0.281 (0.374)	0.0254 (0.0539)	0.227 (0.315)	0.554 (0.636)
11q loss	61 (14%)	380	1e-05 (5.91e-05)	0.0013 (0.0041)	0.927 (0.941)	0.353 (0.453)	0.154 (0.232)	0.105 (0.17)	0.661 (0.736)	0.219 (0.306)	0.0594 (0.108)	0.0165 (0.0371)
18p loss	119 (27%)	322	1e-05 (5.91e-05)	0.038 (0.0749)	0.825 (0.868)	0.112 (0.178)	0.302 (0.397)	0.0363 (0.0732)	0.398 (0.497)	0.179 (0.261)	0.15 (0.227)	0.0883 (0.148)
20p loss	22 (5%)	419	0.0152 (0.0344)	0.00242 (0.00693)	0.00649 (0.0166)	0.685 (0.757)	0.0978 (0.16)	0.119 (0.188)	0.347 (0.447)	0.59 (0.669)	0.708 (0.776)	0.474 (0.567)
3p gain	52 (12%)	389	0.0407 (0.0799)	0.135 (0.21)	0.00974 (0.0235)	0.0608 (0.11)	0.417 (0.515)	0.0978 (0.16)	0.169 (0.249)	0.304 (0.398)	0.232 (0.318)	0.157 (0.235)
4p gain	21 (5%)	420	0.173 (0.254)	0.26 (0.348)	0.286 (0.38)	0.112 (0.178)	0.0415 (0.0812)	0.0736 (0.128)	0.895 (0.915)	0.029 (0.0607)	0.129 (0.201)	0.375 (0.476)
4q gain	16 (4%)	425	0.0974 (0.16)	0.131 (0.204)	0.883 (0.91)	0.162 (0.24)	0.00764 (0.0191)	0.0566 (0.104)	0.232 (0.318)	0.00614 (0.0158)	0.49 (0.583)	0.107 (0.172)
7q gain	171 (39%)	270	1e-05 (5.91e-05)	0.00131 (0.0041)	0.438 (0.534)	0.309 (0.403)	0.188 (0.271)	0.159 (0.237)	0.381 (0.481)	0.221 (0.308)	0.288 (0.381)	0.251 (0.338)
8p gain	183 (41%)	258	0.00238 (0.00684)	0.0015 (0.00455)	0.272 (0.363)	0.256 (0.343)	0.829 (0.869)	0.359 (0.459)	0.434 (0.53)	0.779 (0.838)	0.809 (0.861)	0.996 (0.998)
10q gain	67 (15%)	374	2e-05 (0.000107)	0.0464 (0.0892)	0.661 (0.736)	0.509 (0.599)	0.16 (0.238)	0.0757 (0.131)	0.15 (0.227)	0.105 (0.17)	0.18 (0.261)	0.173 (0.254)
12p gain	92 (21%)	349	0.00041 (0.00151)	0.191 (0.274)	0.24 (0.328)	0.773 (0.833)	0.193 (0.276)	0.231 (0.318)	0.175 (0.256)	0.271 (0.363)	0.0118 (0.0274)	0.33 (0.429)
14q gain	28 (6%)	413	0.0502 (0.0952)	0.239 (0.326)	0.536 (0.621)	0.61 (0.688)	0.494 (0.586)	0.791 (0.848)	0.348 (0.448)	0.518 (0.603)	0.0485 (0.0925)	0.0293 (0.0613)
19p gain	53 (12%)	388	0.00346 (0.00934)	0.857 (0.89)	0.0336 (0.0689)	0.216 (0.303)	0.888 (0.912)	0.953 (0.964)	0.404 (0.504)	0.797 (0.854)	0.73 (0.794)	0.565 (0.644)
xp gain	51 (12%)	390	0.116 (0.182)	0.00271 (0.00762)	0.994 (0.998)	0.499 (0.59)	0.445 (0.54)	0.706 (0.775)	0.0107 (0.0254)	0.39 (0.489)	0.588 (0.668)	0.11 (0.175)
xp loss	61 (14%)	380	1e-05 (5.91e-05)	0.00128 (0.00407)	0.832 (0.869)	0.179 (0.261)	0.108 (0.173)	0.207 (0.291)	0.53 (0.616)	0.158 (0.236)	0.135 (0.21)	0.25 (0.338)
5q gain	43 (10%)	398	0.00156 (0.00471)	0.198 (0.281)	0.61 (0.688)	0.247 (0.335)	0.685 (0.757)	0.937 (0.95)	0.925 (0.94)	0.413 (0.512)	0.888 (0.912)	0.365 (0.464)
12q gain	78 (18%)	363	0.0725 (0.126)	0.546 (0.628)	0.00335 (0.00911)	0.538 (0.621)	0.894 (0.915)	0.541 (0.624)	0.37 (0.471)	0.511 (0.599)	0.283 (0.376)	0.386 (0.485)
16q gain	48 (11%)	393	0.00976 (0.0235)	0.223 (0.309)	0.92 (0.937)	0.167 (0.246)	0.614 (0.691)	0.654 (0.73)	0.91 (0.928)	0.81 (0.861)	0.888 (0.912)	0.0833 (0.142)
22q gain	32 (7%)	409	0.0248 (0.0531)	0.0548 (0.102)	0.596 (0.676)	0.814 (0.864)	0.18 (0.261)	0.205 (0.29)	0.121 (0.19)	0.557 (0.638)	0.444 (0.54)	0.636 (0.713)
13q loss	37 (8%)	404	0.00035 (0.0013)	0.471 (0.564)	0.252 (0.339)	0.0567 (0.104)	0.72 (0.784)	0.189 (0.272)	0.799 (0.855)	0.82 (0.868)	0.406 (0.505)	0.715 (0.782)
9p gain	59 (13%)	382	1 (1.00)	0.801 (0.856)	0.832 (0.869)	0.717 (0.783)	0.867 (0.897)	0.828 (0.869)	0.868 (0.897)	0.681 (0.755)	1 (1.00)	0.282 (0.376)
9q gain	77 (17%)	364	0.408 (0.507)	0.424 (0.523)	0.506 (0.597)	0.772 (0.833)	0.627 (0.705)	0.69 (0.759)	0.563 (0.643)	0.831 (0.869)	0.823 (0.868)	0.458 (0.55)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S1. Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
1P GAIN MUTATED	40	2	7	1
1P GAIN WILD-TYPE	194	151	44	2

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #1: 'CN_CNMF'

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00552 (Fisher's exact test), Q value = 0.014

Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
1P GAIN MUTATED	8	12	2	19	4
1P GAIN WILD-TYPE	37	98	49	81	83

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0016

Table S3. Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
1P GAIN MUTATED	24	6	8	7	3
1P GAIN WILD-TYPE	70	88	85	75	47

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S4. Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
1P GAIN MUTATED	10	2	10	7	3	17
1P GAIN WILD-TYPE	51	64	70	104	47	49

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0058

Table S5. Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
1P GAIN MUTATED	20	6	23
1P GAIN WILD-TYPE	223	76	86

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0045

Table S6. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
1P GAIN MUTATED	24	13	1
1P GAIN WILD-TYPE	123	108	72

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.02

Table S7. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
1P GAIN MUTATED	10	4	1	13	10
1P GAIN WILD-TYPE	93	68	43	49	50

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S8. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
1Q GAIN MUTATED	77	11	16	1
1Q GAIN WILD-TYPE	157	142	35	2

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S9. Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
1Q GAIN MUTATED	16	30	5	37	7
1Q GAIN WILD-TYPE	29	80	46	63	80

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.036

Table S10. Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
1Q GAIN MUTATED	41	14	20	9
1Q GAIN WILD-TYPE	99	44	58	71

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S11. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
1Q GAIN MUTATED	40	15	20	11	13
1Q GAIN WILD-TYPE	54	79	73	71	37

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S12. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
1Q GAIN MUTATED	22	4	22	19	5	31
1Q GAIN WILD-TYPE	39	62	58	92	45	35

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0021

Table S13. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
1Q GAIN MUTATED	46	16	41
1Q GAIN WILD-TYPE	197	66	68

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.0086

Table S14. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
1Q GAIN MUTATED	23	11	5	25	16
1Q GAIN WILD-TYPE	80	61	39	37	44

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S15. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
2P GAIN MUTATED	56	6	15	1
2P GAIN WILD-TYPE	178	147	36	2

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S16. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
2P GAIN MUTATED	5	20	5	35	7
2P GAIN WILD-TYPE	40	90	46	65	80

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.027

Table S17. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
2P GAIN MUTATED	27	9	14	13	11
2P GAIN WILD-TYPE	67	85	79	69	39

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.02

Table S18. Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
2P GAIN MUTATED	15	9	14	12	6	21
2P GAIN WILD-TYPE	46	57	66	99	44	45

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0031

Table S19. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
2P GAIN MUTATED	37	8	32
2P GAIN WILD-TYPE	206	74	77

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.054

Table S20. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
2P GAIN MUTATED	14	6	11	16	13
2P GAIN WILD-TYPE	89	66	33	46	47

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S21. Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
2Q GAIN MUTATED	47	6	12	1
2Q GAIN WILD-TYPE	187	147	39	2

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0024

Table S22. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
2Q GAIN MUTATED	5	17	5	29	6
2Q GAIN WILD-TYPE	40	93	46	71	81

Figure S22. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0061

Table S23. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
2Q GAIN MUTATED	27	8	13	8	8
2Q GAIN WILD-TYPE	67	86	80	74	42

Figure S23. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 0.00751 (Fisher's exact test), Q value = 0.019

Table S24. Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
2Q GAIN MUTATED	13	7	13	11	3	18
2Q GAIN WILD-TYPE	48	59	67	100	47	48

Figure S24. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00898 (Fisher's exact test), Q value = 0.022

Table S25. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
2Q GAIN MUTATED	32	7	26
2Q GAIN WILD-TYPE	211	75	83

Figure S25. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.08

Table S26. Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
3P GAIN MUTATED	37	10	5	0
3P GAIN WILD-TYPE	197	143	46	3

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'CN_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.023

Table S27. Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
3P GAIN MUTATED	6	19	7	10	2
3P GAIN WILD-TYPE	24	73	75	83	57

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'3q gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00071

Table S28. Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
3Q GAIN MUTATED	63	15	12	1
3Q GAIN WILD-TYPE	171	138	39	2

Figure S28. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.028

Table S29. Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
3Q GAIN MUTATED	9	21	14	28	8
3Q GAIN WILD-TYPE	36	89	37	72	79

Figure S29. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.046

Table S30. Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
3Q GAIN MUTATED	30	10	33	13
3Q GAIN WILD-TYPE	79	72	102	74

Figure S30. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.038

Table S31. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
3Q GAIN MUTATED	7	15	19	17	8	23
3Q GAIN WILD-TYPE	54	51	61	94	42	43

Figure S31. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.081

Table S32. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
4P GAIN MUTATED	4	0	5	6	4
4P GAIN WILD-TYPE	90	94	88	76	46

Figure S32. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.061

Table S33. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
4P GAIN MUTATED	17	1	2
4P GAIN WILD-TYPE	226	81	107

Figure S33. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.00764 (Fisher's exact test), Q value = 0.019

Table S34. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
4Q GAIN MUTATED	1	0	5	6	4
4Q GAIN WILD-TYPE	93	94	88	76	46

Figure S34. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00614 (Fisher's exact test), Q value = 0.016

Table S35. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
4Q GAIN MUTATED	15	0	1
4Q GAIN WILD-TYPE	228	82	108

Figure S35. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S36. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
5P GAIN MUTATED	74	11	14	1
5P GAIN WILD-TYPE	160	142	37	2

Figure S36. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S37. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
5P GAIN MUTATED	9	19	7	43	8
5P GAIN WILD-TYPE	36	91	44	57	79

Figure S37. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S38. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
5P GAIN MUTATED	41	10	17	14	12
5P GAIN WILD-TYPE	53	84	76	68	38

Figure S38. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0021

Table S39. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
5P GAIN MUTATED	24	8	45	17
5P GAIN WILD-TYPE	85	74	90	70

Figure S39. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0023

Table S40. Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
5P GAIN MUTATED	14	16	15	15	10	29
5P GAIN WILD-TYPE	47	50	65	96	40	37

Figure S40. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S41. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
5P GAIN MUTATED	45	9	45
5P GAIN WILD-TYPE	198	73	64

Figure S41. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.0011

Table S42. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
5P GAIN MUTATED	23	6	8	26	13
5P GAIN WILD-TYPE	80	66	36	36	47

Figure S42. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0047

Table S43. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
5Q GAIN MUTATED	30	5	7	1
5Q GAIN WILD-TYPE	204	148	44	2

Figure S43. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S44. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
6P GAIN MUTATED	73	4	2	2
6P GAIN WILD-TYPE	161	149	49	1

Figure S44. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S45. Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
6P GAIN MUTATED	7	15	1	41	4
6P GAIN WILD-TYPE	38	95	50	59	83

Figure S45. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S46. Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
6P GAIN MUTATED	36	7	14	9	12
6P GAIN WILD-TYPE	58	87	79	73	38

Figure S46. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00474 (Fisher's exact test), Q value = 0.012

Table S47. Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
6P GAIN MUTATED	23	5	31	19
6P GAIN WILD-TYPE	86	77	104	68

Figure S47. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S48. Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
6P GAIN MUTATED	14	10	15	7	4	30
6P GAIN WILD-TYPE	47	56	65	104	46	36

Figure S48. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S49. Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
6P GAIN MUTATED	36	6	38
6P GAIN WILD-TYPE	207	76	71

Figure S49. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S50. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
6P GAIN MUTATED	10	6	6	23	14
6P GAIN WILD-TYPE	93	66	38	39	46

Figure S50. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S51. Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
6Q GAIN MUTATED	58	5	2	1
6Q GAIN WILD-TYPE	176	148	49	2

Figure S51. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S52. Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
6Q GAIN MUTATED	5	14	1	33	2
6Q GAIN WILD-TYPE	40	96	50	67	85

Figure S52. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.075

Table S53. Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
6Q GAIN MUTATED	4	21	17	8	6
6Q GAIN WILD-TYPE	26	71	65	85	53

Figure S53. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S54. Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
6Q GAIN MUTATED	31	7	8	6	12
6Q GAIN WILD-TYPE	63	87	85	76	38

Figure S54. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.045

Table S55. Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
6Q GAIN MUTATED	15	5	27	17
6Q GAIN WILD-TYPE	94	77	108	70

Figure S55. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S56. Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
6Q GAIN MUTATED	15	8	9	6	4	23
6Q GAIN WILD-TYPE	46	58	71	105	46	43

Figure S56. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00071

Table S57. Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
6Q GAIN MUTATED	31	5	29
6Q GAIN WILD-TYPE	212	77	80

Figure S57. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S58. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
6Q GAIN MUTATED	8	4	3	19	14
6Q GAIN WILD-TYPE	95	68	41	43	46

Figure S58. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S59. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
7P GAIN MUTATED	123	30	47	2
7P GAIN WILD-TYPE	111	123	4	1

Figure S59. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S60. Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
7P GAIN MUTATED	20	56	22	62	21
7P GAIN WILD-TYPE	25	54	29	38	66

Figure S60. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.019

Table S61. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
7P GAIN MUTATED	51	32	40	35	31
7P GAIN WILD-TYPE	43	62	53	47	19

Figure S61. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0427 (Fisher's exact test), Q value = 0.083

Table S62. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
7P GAIN MUTATED	50	27	65	47
7P GAIN WILD-TYPE	59	55	70	40

Figure S62. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.026

Table S63. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
7P GAIN MUTATED	113	26	58
7P GAIN WILD-TYPE	130	56	51

Figure S63. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00817 (Fisher's exact test), Q value = 0.02

Table S64. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
7P GAIN MUTATED	50	19	19	33	31
7P GAIN WILD-TYPE	53	53	25	29	29

Figure S64. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S65. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
7Q GAIN MUTATED	98	28	45	0
7Q GAIN WILD-TYPE	136	125	6	3

Figure S65. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0041

Table S66. Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
7Q GAIN MUTATED	16	42	21	51	19
7Q GAIN WILD-TYPE	29	68	30	49	68

Figure S66. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0068

Table S67. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
8P GAIN MUTATED	81	77	22	3
8P GAIN WILD-TYPE	153	76	29	0

Figure S67. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0046

Table S68. Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
8P GAIN MUTATED	11	61	17	40	30
8P GAIN WILD-TYPE	34	49	34	60	57

Figure S68. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S69. Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
8Q GAIN MUTATED	17	75	20	64	37
8Q GAIN WILD-TYPE	28	35	31	36	50

Figure S69. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.03

Table S70. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
8Q GAIN MUTATED	37	38	41	47	27	46
8Q GAIN WILD-TYPE	24	28	39	64	23	20

Figure S70. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.071

Table S71. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
8Q GAIN MUTATED	128	38	70
8Q GAIN WILD-TYPE	115	44	39

Figure S71. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S72. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
10P GAIN MUTATED	80	8	10	0
10P GAIN WILD-TYPE	154	145	41	3

Figure S72. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S73. Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
10P GAIN MUTATED	10	22	3	38	13
10P GAIN WILD-TYPE	35	88	48	62	74

Figure S73. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.019

Table S74. Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
10P GAIN MUTATED	35	17	18	14	9
10P GAIN WILD-TYPE	59	77	75	68	41

Figure S74. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0021

Table S75. Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
10P GAIN MUTATED	39	18	38
10P GAIN WILD-TYPE	204	64	71

Figure S75. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.036

Table S76. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
10P GAIN MUTATED	18	11	7	23	16
10P GAIN WILD-TYPE	85	61	37	39	44

Figure S76. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S77. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
10Q GAIN MUTATED	54	8	5	0
10Q GAIN WILD-TYPE	180	145	46	3

Figure S77. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.089

Table S78. Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
10Q GAIN MUTATED	9	16	3	22	9
10Q GAIN WILD-TYPE	36	94	48	78	78

Figure S78. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S79. Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
11P GAIN MUTATED	54	5	3	0
11P GAIN WILD-TYPE	180	148	48	3

Figure S79. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00046

Table S80. Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
11P GAIN MUTATED	5	9	7	29	6
11P GAIN WILD-TYPE	40	101	44	71	81

Figure S80. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00082

Table S81. Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
11P GAIN MUTATED	11	6	10	7	4	21
11P GAIN WILD-TYPE	50	60	70	104	46	45

Figure S81. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.001

Table S82. Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
11P GAIN MUTATED	26	5	28
11P GAIN WILD-TYPE	217	77	81

Figure S82. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.023

Table S83. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
11P GAIN MUTATED	11	4	4	16	10
11P GAIN WILD-TYPE	92	68	40	46	50

Figure S83. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S84. Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
11Q GAIN MUTATED	66	7	1	0
11Q GAIN WILD-TYPE	168	146	50	3

Figure S84. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00036

Table S85. Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
11Q GAIN MUTATED	5	15	7	32	6
11Q GAIN WILD-TYPE	40	95	44	68	81

Figure S85. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.073

Table S86. Gene #22: '11q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
11Q GAIN MUTATED	2	23	16	10	7
11Q GAIN WILD-TYPE	28	69	66	83	52

Figure S86. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.046

Table S87. Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
11Q GAIN MUTATED	25	8	14	16	8
11Q GAIN WILD-TYPE	69	86	79	66	42

Figure S87. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00678 (Fisher's exact test), Q value = 0.017

Table S88. Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
11Q GAIN MUTATED	19	5	32	15
11Q GAIN WILD-TYPE	90	77	103	72

Figure S88. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00024

Table S89. Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
11Q GAIN MUTATED	13	9	12	6	8	23
11Q GAIN WILD-TYPE	48	57	68	105	42	43

Figure S89. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00028

Table S90. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
11Q GAIN MUTATED	36	4	31
11Q GAIN WILD-TYPE	207	78	78

Figure S90. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.039

Table S91. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
11Q GAIN MUTATED	33	14	7
11Q GAIN WILD-TYPE	114	107	66

Figure S91. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00032

Table S92. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
11Q GAIN MUTATED	11	3	5	18	17
11Q GAIN WILD-TYPE	92	69	39	44	43

Figure S92. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0015

Table S93. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
12P GAIN MUTATED	57	17	17	1
12P GAIN WILD-TYPE	177	136	34	2

Figure S93. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.027

Table S94. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
12P GAIN MUTATED	42	17	13
12P GAIN WILD-TYPE	105	104	60

Figure S94. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'RPPA_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0091

Table S95. Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
12Q GAIN MUTATED	7	9	16	7	16
12Q GAIN WILD-TYPE	23	83	66	86	43

Figure S95. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S96. Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
13Q GAIN MUTATED	102	22	29	0
13Q GAIN WILD-TYPE	132	131	22	3

Figure S96. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S97. Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
13Q GAIN MUTATED	13	34	9	56	23
13Q GAIN WILD-TYPE	32	76	42	44	64

Figure S97. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S98. Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
13Q GAIN MUTATED	47	23	31	15	28
13Q GAIN WILD-TYPE	47	71	62	67	22

Figure S98. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00384 (Fisher's exact test), Q value = 0.01

Table S99. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
13Q GAIN MUTATED	32	20	49	43
13Q GAIN WILD-TYPE	77	62	86	44

Figure S99. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S100. Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
13Q GAIN MUTATED	30	18	25	28	9	38
13Q GAIN WILD-TYPE	31	48	55	83	41	28

Figure S100. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0021

Table S101. Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
13Q GAIN MUTATED	70	24	54
13Q GAIN WILD-TYPE	173	58	55

Figure S101. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.011

Table S102. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
13Q GAIN MUTATED	31	19	12	34	17
13Q GAIN WILD-TYPE	72	53	32	28	43

Figure S102. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0485 (Fisher's exact test), Q value = 0.092

Table S103. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
14Q GAIN MUTATED	14	6	1
14Q GAIN WILD-TYPE	133	115	72

Figure S103. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.061

Table S104. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
14Q GAIN MUTATED	4	3	0	8	6
14Q GAIN WILD-TYPE	99	69	44	54	54

Figure S104. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S105. Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
15Q GAIN MUTATED	34	1	4	0
15Q GAIN WILD-TYPE	200	152	47	3

Figure S105. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.006

Table S106. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
15Q GAIN MUTATED	7	6	1	17	4
15Q GAIN WILD-TYPE	38	104	50	83	83

Figure S106. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0233 (Fisher's exact test), Q value = 0.05

Table S107. Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
15Q GAIN MUTATED	15	3	7	5	6
15Q GAIN WILD-TYPE	79	91	86	77	44

Figure S107. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.075

Table S108. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
15Q GAIN MUTATED	8	2	18	8
15Q GAIN WILD-TYPE	101	80	117	79

Figure S108. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00313 (Fisher's exact test), Q value = 0.0086

Table S109. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
15Q GAIN MUTATED	16	3	18
15Q GAIN WILD-TYPE	227	79	91

Figure S109. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00623 (Fisher's exact test), Q value = 0.016

Table S110. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
15Q GAIN MUTATED	5	1	7	9	6
15Q GAIN WILD-TYPE	98	71	37	53	54

Figure S110. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S111. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
16P GAIN MUTATED	42	9	7	0
16P GAIN WILD-TYPE	192	144	44	3

Figure S111. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.049 (Fisher's exact test), Q value = 0.093

Table S112. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
16P GAIN MUTATED	9	9	4	19	8
16P GAIN WILD-TYPE	36	101	47	81	79

Figure S112. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.027

Table S113. Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
16P GAIN MUTATED	27	3	5	10
16P GAIN WILD-TYPE	113	55	73	70

Figure S113. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00976 (Fisher's exact test), Q value = 0.023

Table S114. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
16Q GAIN MUTATED	34	7	7	0
16Q GAIN WILD-TYPE	200	146	44	3

Figure S114. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0076

Table S115. Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
17P GAIN MUTATED	23	3	2	1
17P GAIN WILD-TYPE	211	150	49	2

Figure S115. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.021

Table S116. Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
17P GAIN MUTATED	5	6	4	10	0
17P GAIN WILD-TYPE	40	104	47	90	87

Figure S116. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.053

Table S117. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
17P GAIN MUTATED	5	0	4	7	4
17P GAIN WILD-TYPE	98	72	40	55	56

Figure S117. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S118. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
17Q GAIN MUTATED	53	5	5	1
17Q GAIN WILD-TYPE	181	148	46	2

Figure S118. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0027

Table S119. Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
17Q GAIN MUTATED	12	15	11	18	3
17Q GAIN WILD-TYPE	33	95	40	82	84

Figure S119. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.0017

Table S120. Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
17Q GAIN MUTATED	21	5	19	13	2
17Q GAIN WILD-TYPE	73	89	74	69	48

Figure S120. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00529 (Fisher's exact test), Q value = 0.014

Table S121. Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
17Q GAIN MUTATED	17	6	30	7
17Q GAIN WILD-TYPE	92	76	105	80

Figure S121. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.048

Table S122. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
17Q GAIN MUTATED	18	3	7	13	6
17Q GAIN WILD-TYPE	85	69	37	49	54

Figure S122. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S123. Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
18P GAIN MUTATED	63	12	10	0
18P GAIN WILD-TYPE	171	141	41	3

Figure S123. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S124. Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
18P GAIN MUTATED	10	17	2	38	9
18P GAIN WILD-TYPE	35	93	49	62	78

Figure S124. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0021

Table S125. Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
18P GAIN MUTATED	40	8	9	7
18P GAIN WILD-TYPE	100	50	69	73

Figure S125. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S126. Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
18P GAIN MUTATED	32	10	9	20	10
18P GAIN WILD-TYPE	62	84	84	62	40

Figure S126. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.084

Table S127. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
18P GAIN MUTATED	28	8	27	18
18P GAIN WILD-TYPE	81	74	108	69

Figure S127. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.001

Table S128. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
18P GAIN MUTATED	12	10	11	14	10	28
18P GAIN WILD-TYPE	49	56	69	97	40	38

Figure S128. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00024

Table S129. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
18P GAIN MUTATED	38	9	38
18P GAIN WILD-TYPE	205	73	71

Figure S129. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0012

Table S130. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
18P GAIN MUTATED	43	12	12
18P GAIN WILD-TYPE	104	109	61

Figure S130. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00324 (Fisher's exact test), Q value = 0.0089

Table S131. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
18P GAIN MUTATED	14	8	7	19	19
18P GAIN WILD-TYPE	89	64	37	43	41

Figure S131. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.075

Table S132. Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
18Q GAIN MUTATED	39	11	5	0
18Q GAIN WILD-TYPE	195	142	46	3

Figure S132. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.027

Table S133. Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
18Q GAIN MUTATED	6	12	2	22	7
18Q GAIN WILD-TYPE	39	98	49	78	80

Figure S133. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.031

Table S134. Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
18Q GAIN MUTATED	19	8	5	14	6
18Q GAIN WILD-TYPE	75	86	88	68	44

Figure S134. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S135. Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
18Q GAIN MUTATED	24	8	23
18Q GAIN WILD-TYPE	219	74	86

Figure S135. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 0.00346 (Fisher's exact test), Q value = 0.0093

Table S136. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
19P GAIN MUTATED	34	8	11	0
19P GAIN WILD-TYPE	200	145	40	3

Figure S136. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.069

Table S137. Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
19P GAIN MUTATED	4	9	14	5	12
19P GAIN WILD-TYPE	26	83	68	88	47

Figure S137. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S138. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
19Q GAIN MUTATED	54	10	15	0
19Q GAIN WILD-TYPE	180	143	36	3

Figure S138. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S139. Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
19Q GAIN MUTATED	6	14	22	7	12
19Q GAIN WILD-TYPE	24	78	60	86	47

Figure S139. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.051

Table S140. Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
19Q GAIN MUTATED	34	9	11	7
19Q GAIN WILD-TYPE	106	49	67	73

Figure S140. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.084

Table S141. Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
19Q GAIN MUTATED	13	9	16	15	5	20
19Q GAIN WILD-TYPE	48	57	64	96	45	46

Figure S141. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.075

Table S142. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
19Q GAIN MUTATED	35	16	9
19Q GAIN WILD-TYPE	112	105	64

Figure S142. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00885 (Fisher's exact test), Q value = 0.022

Table S143. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
19Q GAIN MUTATED	20	7	5	20	8
19Q GAIN WILD-TYPE	83	65	39	42	52

Figure S143. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S144. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
20P GAIN MUTATED	166	40	33	3
20P GAIN WILD-TYPE	68	113	18	0

Figure S144. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S145. Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
20P GAIN MUTATED	24	49	32	80	30
20P GAIN WILD-TYPE	21	61	19	20	57

Figure S145. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.041

Table S146. Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
20P GAIN MUTATED	87	27	46	34
20P GAIN WILD-TYPE	53	31	32	46

Figure S146. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S147. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
20P GAIN MUTATED	73	43	40	42	31
20P GAIN WILD-TYPE	21	51	53	40	19

Figure S147. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S148. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
20P GAIN MUTATED	53	34	99	43
20P GAIN WILD-TYPE	56	48	36	44

Figure S148. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S149. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
20P GAIN MUTATED	30	32	45	53	22	56
20P GAIN WILD-TYPE	31	34	35	58	28	10

Figure S149. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S150. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
20P GAIN MUTATED	118	37	83
20P GAIN WILD-TYPE	125	45	26

Figure S150. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00036

Table S151. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
20P GAIN MUTATED	46	34	20	50	31
20P GAIN WILD-TYPE	57	38	24	12	29

Figure S151. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S152. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
20Q GAIN MUTATED	195	44	38	3
20Q GAIN WILD-TYPE	39	109	13	0

Figure S152. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S153. Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
20Q GAIN MUTATED	33	54	35	94	36
20Q GAIN WILD-TYPE	12	56	16	6	51

Figure S153. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0044

Table S154. Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
20Q GAIN MUTATED	102	28	52	42
20Q GAIN WILD-TYPE	38	30	26	38

Figure S154. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S155. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
20Q GAIN MUTATED	89	46	45	51	35
20Q GAIN WILD-TYPE	5	48	48	31	15

Figure S155. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S156. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
20Q GAIN MUTATED	68	38	112	48
20Q GAIN WILD-TYPE	41	44	23	39

Figure S156. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S157. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
20Q GAIN MUTATED	35	35	53	61	29	62
20Q GAIN WILD-TYPE	26	31	27	50	21	4

Figure S157. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S158. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
20Q GAIN MUTATED	136	41	98
20Q GAIN WILD-TYPE	107	41	11

Figure S158. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S159. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
20Q GAIN MUTATED	53	38	28	58	38
20Q GAIN WILD-TYPE	50	34	16	4	22

Figure S159. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0019

Table S160. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
21Q GAIN MUTATED	19	0	3	0
21Q GAIN WILD-TYPE	215	153	48	3

Figure S160. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.012

Table S161. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
21Q GAIN MUTATED	3	5	0	12	1
21Q GAIN WILD-TYPE	42	105	51	88	86

Figure S161. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00082

Table S162. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
21Q GAIN MUTATED	12	1	1	2	5
21Q GAIN WILD-TYPE	82	93	92	80	45

Figure S162. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.058

Table S163. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
21Q GAIN MUTATED	3	4	2	2	2	9
21Q GAIN WILD-TYPE	58	62	78	109	48	57

Figure S163. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.002

Table S164. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
21Q GAIN MUTATED	9	0	13
21Q GAIN WILD-TYPE	234	82	96

Figure S164. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.0068

Table S165. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
21Q GAIN MUTATED	3	0	3	9	4
21Q GAIN WILD-TYPE	100	72	41	53	56

Figure S165. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 0.0248 (Fisher's exact test), Q value = 0.053

Table S166. Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
22Q GAIN MUTATED	22	4	6	0
22Q GAIN WILD-TYPE	212	149	45	3

Figure S166. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0076

Table S167. Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
XP GAIN MUTATED	9	14	2	17	3
XP GAIN WILD-TYPE	36	96	49	83	84

Figure S167. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.025

Table S168. Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
XP GAIN MUTATED	11	6	11	6	2	13
XP GAIN WILD-TYPE	50	60	69	105	48	53

Figure S168. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.066

Table S169. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
XQ GAIN MUTATED	31	12	12	0
XQ GAIN WILD-TYPE	203	141	39	3

Figure S169. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 0.0306 (Fisher's exact test), Q value = 0.064

Table S170. Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
XQ GAIN MUTATED	6	17	3	19	5
XQ GAIN WILD-TYPE	39	93	48	81	82

Figure S170. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.049

Table S171. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
XQ GAIN MUTATED	13	10	10	19
XQ GAIN WILD-TYPE	96	72	125	68

Figure S171. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.073

Table S172. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
XQ GAIN MUTATED	14	7	8	8	4	12
XQ GAIN WILD-TYPE	47	59	72	103	46	54

Figure S172. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S173. Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
1P LOSS MUTATED	54	1	3	0
1P LOSS WILD-TYPE	180	152	48	3

Figure S173. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S174. Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
1P LOSS MUTATED	10	12	2	25	4
1P LOSS WILD-TYPE	35	98	49	75	83

Figure S174. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.0042

Table S175. Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
1P LOSS MUTATED	20	4	12	6	10
1P LOSS WILD-TYPE	74	90	81	76	40

Figure S175. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00309 (Fisher's exact test), Q value = 0.0086

Table S176. Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
1P LOSS MUTATED	8	4	26	14
1P LOSS WILD-TYPE	101	78	109	73

Figure S176. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.012

Table S177. Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
1P LOSS MUTATED	4	11	10	10	3	18
1P LOSS WILD-TYPE	57	55	70	101	47	48

Figure S177. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00689 (Fisher's exact test), Q value = 0.017

Table S178. Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
1P LOSS MUTATED	25	7	24
1P LOSS WILD-TYPE	218	75	85

Figure S178. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00489 (Fisher's exact test), Q value = 0.013

Table S179. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
1P LOSS MUTATED	11	4	7	16	4
1P LOSS WILD-TYPE	92	68	37	46	56

Figure S179. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S180. Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
1Q LOSS MUTATED	24	1	0	0
1Q LOSS WILD-TYPE	210	152	51	3

Figure S180. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 5e-04

Table S181. Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
1Q LOSS MUTATED	6	4	1	13	0
1Q LOSS WILD-TYPE	39	106	50	87	87

Figure S181. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.025

Table S182. Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
1Q LOSS MUTATED	4	1	15	3
1Q LOSS WILD-TYPE	105	81	120	84

Figure S182. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0044

Table S183. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
1Q LOSS MUTATED	4	0	6	7	1
1Q LOSS WILD-TYPE	99	72	38	55	59

Figure S183. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00065

Table S184. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
2P LOSS MUTATED	21	0	2	0
2P LOSS WILD-TYPE	213	153	49	3

Figure S184. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00028

Table S185. Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
2P LOSS MUTATED	9	3	0	9	1
2P LOSS WILD-TYPE	36	107	51	91	86

Figure S185. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.064

Table S186. Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
2P LOSS MUTATED	11	4	1	4	2
2P LOSS WILD-TYPE	83	90	92	78	48

Figure S186. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.091

Table S187. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
2P LOSS MUTATED	12	2	5
2P LOSS WILD-TYPE	135	119	68

Figure S187. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S188. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
2Q LOSS MUTATED	28	0	2	0
2Q LOSS WILD-TYPE	206	153	49	3

Figure S188. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00071

Table S189. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
2Q LOSS MUTATED	9	5	0	11	2
2Q LOSS WILD-TYPE	36	105	51	89	85

Figure S189. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.054

Table S190. Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
2Q LOSS MUTATED	13	3	14
2Q LOSS WILD-TYPE	230	79	95

Figure S190. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S191. Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
3P LOSS MUTATED	78	2	10	3
3P LOSS WILD-TYPE	156	151	41	0

Figure S191. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00075

Table S192. Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
3P LOSS MUTATED	11	24	5	36	9
3P LOSS WILD-TYPE	34	86	46	64	78

Figure S192. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S193. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
3P LOSS MUTATED	36	11	12	10	15
3P LOSS WILD-TYPE	58	83	81	72	35

Figure S193. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0086

Table S194. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
3P LOSS MUTATED	15	9	37	23
3P LOSS WILD-TYPE	94	73	98	64

Figure S194. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.081

Table S195. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
3P LOSS MUTATED	17	9	16	20	7	22
3P LOSS WILD-TYPE	44	57	64	91	43	44

Figure S195. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.0028

Table S196. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
3P LOSS MUTATED	42	12	37
3P LOSS WILD-TYPE	201	70	72

Figure S196. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00131 (Fisher's exact test), Q value = 0.0041

Table S197. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
3P LOSS MUTATED	21	7	8	24	9
3P LOSS WILD-TYPE	82	65	36	38	51

Figure S197. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S198. Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
3Q LOSS MUTATED	45	0	9	2
3Q LOSS WILD-TYPE	189	153	42	1

Figure S198. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S199. Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
3Q LOSS MUTATED	8	15	1	23	4
3Q LOSS WILD-TYPE	37	95	50	77	83

Figure S199. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S200. Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
3Q LOSS MUTATED	24	6	8	1	13
3Q LOSS WILD-TYPE	70	88	85	81	37

Figure S200. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S201. Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
3Q LOSS MUTATED	2	6	25	19
3Q LOSS WILD-TYPE	107	76	110	68

Figure S201. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0045

Table S202. Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
3Q LOSS MUTATED	15	2	9	14	2	12
3Q LOSS WILD-TYPE	46	64	71	97	48	54

Figure S202. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S203. Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
3Q LOSS MUTATED	23	8	23
3Q LOSS WILD-TYPE	220	74	86

Figure S203. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00032

Table S204. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
3Q LOSS MUTATED	15	4	4	17	1
3Q LOSS WILD-TYPE	88	68	40	45	59

Figure S204. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S205. Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
4P LOSS MUTATED	146	7	13	1
4P LOSS WILD-TYPE	88	146	38	2

Figure S205. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S206. Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
4P LOSS MUTATED	23	33	7	60	24
4P LOSS WILD-TYPE	22	77	44	40	63

Figure S206. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S207. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
4P LOSS MUTATED	60	27	29	25	15
4P LOSS WILD-TYPE	34	67	64	57	35

Figure S207. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S208. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
4P LOSS MUTATED	23	16	25	37	18	47
4P LOSS WILD-TYPE	38	50	55	74	32	19

Figure S208. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S209. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
4P LOSS MUTATED	69	26	71
4P LOSS WILD-TYPE	174	56	38

Figure S209. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.023

Table S210. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
4P LOSS MUTATED	67	45	18
4P LOSS WILD-TYPE	80	76	55

Figure S210. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S211. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
4P LOSS MUTATED	34	21	9	42	24
4P LOSS WILD-TYPE	69	51	35	20	36

Figure S211. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S212. Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
4Q LOSS MUTATED	150	6	8	1
4Q LOSS WILD-TYPE	84	147	43	2

Figure S212. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S213. Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
4Q LOSS MUTATED	22	35	7	60	24
4Q LOSS WILD-TYPE	23	75	44	40	63

Figure S213. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S214. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
4Q LOSS MUTATED	58	27	30	24	14
4Q LOSS WILD-TYPE	36	67	63	58	36

Figure S214. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.055

Table S215. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
4Q LOSS MUTATED	36	27	64	26
4Q LOSS WILD-TYPE	73	55	71	61

Figure S215. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S216. Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
4Q LOSS MUTATED	23	16	24	37	18	45
4Q LOSS WILD-TYPE	38	50	56	74	32	21

Figure S216. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S217. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
4Q LOSS MUTATED	69	25	69
4Q LOSS WILD-TYPE	174	57	40

Figure S217. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S218. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
4Q LOSS MUTATED	33	21	13	43	21
4Q LOSS WILD-TYPE	70	51	31	19	39

Figure S218. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S219. Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
5P LOSS MUTATED	57	1	4	1
5P LOSS WILD-TYPE	177	152	47	2

Figure S219. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S220. Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
5P LOSS MUTATED	3	19	1	30	5
5P LOSS WILD-TYPE	42	91	50	70	82

Figure S220. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S221. Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
5P LOSS MUTATED	31	7	9	5	7
5P LOSS WILD-TYPE	63	87	84	77	43

Figure S221. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0021

Table S222. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
5P LOSS MUTATED	11	4	32	12
5P LOSS WILD-TYPE	98	78	103	75

Figure S222. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S223. Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
5P LOSS MUTATED	13	4	8	9	4	23
5P LOSS WILD-TYPE	48	62	72	102	46	43

Figure S223. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S224. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
5P LOSS MUTATED	24	6	31
5P LOSS WILD-TYPE	219	76	78

Figure S224. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S225. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
5P LOSS MUTATED	13	4	5	23	7
5P LOSS WILD-TYPE	90	68	39	39	53

Figure S225. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S226. Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
5Q LOSS MUTATED	98	1	8	1
5Q LOSS WILD-TYPE	136	152	43	2

Figure S226. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S227. Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
5Q LOSS MUTATED	7	25	4	55	10
5Q LOSS WILD-TYPE	38	85	47	45	77

Figure S227. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S228. Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
5Q LOSS MUTATED	55	8	15	15	10
5Q LOSS WILD-TYPE	39	86	78	67	40

Figure S228. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S229. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
5Q LOSS MUTATED	23	5	58	17
5Q LOSS WILD-TYPE	86	77	77	70

Figure S229. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S230. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
5Q LOSS MUTATED	15	8	13	15	13	41
5Q LOSS WILD-TYPE	46	58	67	96	37	25

Figure S230. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S231. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
5Q LOSS MUTATED	42	9	54
5Q LOSS WILD-TYPE	201	73	55

Figure S231. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S232. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
5Q LOSS MUTATED	24	6	8	39	14
5Q LOSS WILD-TYPE	79	66	36	23	46

Figure S232. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S233. Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
6P LOSS MUTATED	40	3	7	0
6P LOSS WILD-TYPE	194	150	44	3

Figure S233. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 4e-04

Table S234. Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
6P LOSS MUTATED	11	12	0	19	5
6P LOSS WILD-TYPE	34	98	51	81	82

Figure S234. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.028

Table S235. Gene #52: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
6P LOSS MUTATED	1	9	12	4	12
6P LOSS WILD-TYPE	29	83	70	89	47

Figure S235. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0064

Table S236. Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
6P LOSS MUTATED	18	3	8	14	4
6P LOSS WILD-TYPE	76	91	85	68	46

Figure S236. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.063

Table S237. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
6P LOSS MUTATED	15	3	21	8
6P LOSS WILD-TYPE	94	79	114	79

Figure S237. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.026

Table S238. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
6P LOSS MUTATED	25	4	20
6P LOSS WILD-TYPE	218	78	89

Figure S238. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S239. Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
6Q LOSS MUTATED	53	5	10	1
6Q LOSS WILD-TYPE	181	148	41	2

Figure S239. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S240. Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
6Q LOSS MUTATED	16	13	2	22	9
6Q LOSS WILD-TYPE	29	97	49	78	78

Figure S240. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0028

Table S241. Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
6Q LOSS MUTATED	21	6	12	21	4
6Q LOSS WILD-TYPE	73	88	81	61	46

Figure S241. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.012

Table S242. Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
6Q LOSS MUTATED	24	5	26	9
6Q LOSS WILD-TYPE	85	77	109	78

Figure S242. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.072

Table S243. Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
6Q LOSS MUTATED	36	7	24
6Q LOSS WILD-TYPE	207	75	85

Figure S243. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0022

Table S244. Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
7P LOSS MUTATED	17	0	0	0
7P LOSS WILD-TYPE	217	153	51	3

Figure S244. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0052

Table S245. Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
7P LOSS MUTATED	3	1	1	9	0
7P LOSS WILD-TYPE	42	109	50	91	87

Figure S245. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 0.00228 (Fisher's exact test), Q value = 0.0066

Table S246. Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
7P LOSS MUTATED	11	2	1	1	2
7P LOSS WILD-TYPE	83	92	92	81	48

Figure S246. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0025

Table S247. Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
7P LOSS MUTATED	2	1	0	2	3	9
7P LOSS WILD-TYPE	59	65	80	109	47	57

Figure S247. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.011

Table S248. Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
7P LOSS MUTATED	4	3	10
7P LOSS WILD-TYPE	239	79	99

Figure S248. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.073

Table S249. Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
7P LOSS MUTATED	2	1	0	5	5
7P LOSS WILD-TYPE	101	71	44	57	55

Figure S249. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S250. Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
7Q LOSS MUTATED	29	0	0	0
7Q LOSS WILD-TYPE	205	153	51	3

Figure S250. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #1: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0012

Table S251. Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
7Q LOSS MUTATED	5	6	1	14	0
7Q LOSS WILD-TYPE	40	104	50	86	87

Figure S251. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00036

Table S252. Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
7Q LOSS MUTATED	18	3	3	3	2
7Q LOSS WILD-TYPE	76	91	90	79	48

Figure S252. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00054

Table S253. Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
7Q LOSS MUTATED	4	2	1	3	5	13
7Q LOSS WILD-TYPE	57	64	79	108	45	53

Figure S253. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.0071

Table S254. Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
7Q LOSS MUTATED	9	4	15
7Q LOSS WILD-TYPE	234	78	94

Figure S254. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S255. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
8P LOSS MUTATED	73	4	14	0
8P LOSS WILD-TYPE	161	149	37	3

Figure S255. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0018

Table S256. Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
8P LOSS MUTATED	17	19	4	29	12
8P LOSS WILD-TYPE	28	91	47	71	75

Figure S256. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.074

Table S257. Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
8P LOSS MUTATED	11	17	22	12	12
8P LOSS WILD-TYPE	19	75	60	81	47

Figure S257. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.071

Table S258. Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
8P LOSS MUTATED	38	14	12	10
8P LOSS WILD-TYPE	102	44	66	70

Figure S258. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00089

Table S259. Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
8P LOSS MUTATED	28	7	16	20	16
8P LOSS WILD-TYPE	66	87	77	62	34

Figure S259. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00071

Table S260. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
8P LOSS MUTATED	28	4	34	21
8P LOSS WILD-TYPE	81	78	101	66

Figure S260. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.032

Table S261. Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
8P LOSS MUTATED	18	11	17	12	15	16
8P LOSS WILD-TYPE	43	55	63	99	35	50

Figure S261. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0041

Table S262. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
8P LOSS MUTATED	54	6	29
8P LOSS WILD-TYPE	189	76	80

Figure S262. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.019

Table S263. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
8P LOSS MUTATED	41	15	15
8P LOSS WILD-TYPE	106	106	58

Figure S263. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S264. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
8P LOSS MUTATED	32	3	7	15	14
8P LOSS WILD-TYPE	71	69	37	47	46

Figure S264. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S265. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
8Q LOSS MUTATED	30	0	7	0
8Q LOSS WILD-TYPE	204	153	44	3

Figure S265. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.039

Table S266. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
8Q LOSS MUTATED	8	2	8	9	9
8Q LOSS WILD-TYPE	86	92	85	73	41

Figure S266. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.045

Table S267. Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
8Q LOSS MUTATED	9	7	6	5	7	1
8Q LOSS WILD-TYPE	52	59	74	106	43	65

Figure S267. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.084

Table S268. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
8Q LOSS MUTATED	14	3	1	2	6
8Q LOSS WILD-TYPE	89	69	43	60	54

Figure S268. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S269. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
9P LOSS MUTATED	135	1	12	1
9P LOSS WILD-TYPE	99	152	39	2

Figure S269. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S270. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
9P LOSS MUTATED	23	30	1	60	21
9P LOSS WILD-TYPE	22	80	50	40	66

Figure S270. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00028

Table S271. Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
9P LOSS MUTATED	65	9	22	24
9P LOSS WILD-TYPE	75	49	56	56

Figure S271. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S272. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
9P LOSS MUTATED	59	20	20	29	15
9P LOSS WILD-TYPE	35	74	73	53	35

Figure S272. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 5e-04

Table S273. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
9P LOSS MUTATED	42	17	63	21
9P LOSS WILD-TYPE	67	65	72	66

Figure S273. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S274. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
9P LOSS MUTATED	20	13	19	32	19	43
9P LOSS WILD-TYPE	41	53	61	79	31	23

Figure S274. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S275. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
9P LOSS MUTATED	66	19	61
9P LOSS WILD-TYPE	177	63	48

Figure S275. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00046

Table S276. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
9P LOSS MUTATED	32	16	15	38	20
9P LOSS WILD-TYPE	71	56	29	24	40

Figure S276. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S277. Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
9Q LOSS MUTATED	94	1	8	1
9Q LOSS WILD-TYPE	140	152	43	2

Figure S277. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S278. Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
9Q LOSS MUTATED	17	16	2	42	17
9Q LOSS WILD-TYPE	28	94	49	58	70

Figure S278. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00337 (Fisher's exact test), Q value = 0.0091

Table S279. Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
9Q LOSS MUTATED	45	5	17	17
9Q LOSS WILD-TYPE	95	53	61	63

Figure S279. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S280. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
9Q LOSS MUTATED	46	17	12	19	8
9Q LOSS WILD-TYPE	48	77	81	63	42

Figure S280. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0036

Table S281. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
9Q LOSS MUTATED	28	13	48	13
9Q LOSS WILD-TYPE	81	69	87	74

Figure S281. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S282. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
9Q LOSS MUTATED	13	9	15	22	10	33
9Q LOSS WILD-TYPE	48	57	65	89	40	33

Figure S282. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S283. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
9Q LOSS MUTATED	44	12	46
9Q LOSS WILD-TYPE	199	70	63

Figure S283. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.073

Table S284. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
9Q LOSS MUTATED	43	28	10
9Q LOSS WILD-TYPE	104	93	63

Figure S284. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S285. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
9Q LOSS MUTATED	19	9	8	30	15
9Q LOSS WILD-TYPE	84	63	36	32	45

Figure S285. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S286. Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
10P LOSS MUTATED	49	3	11	1
10P LOSS WILD-TYPE	185	150	40	2

Figure S286. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0038

Table S287. Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
10P LOSS MUTATED	10	14	1	23	8
10P LOSS WILD-TYPE	35	96	50	77	79

Figure S287. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.005

Table S288. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
10P LOSS MUTATED	24	6	10	16	5
10P LOSS WILD-TYPE	70	88	83	66	45

Figure S288. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0042

Table S289. Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
10P LOSS MUTATED	23	3	25	10
10P LOSS WILD-TYPE	86	79	110	77

Figure S289. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0035

Table S290. Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
10P LOSS MUTATED	8	6	16	6	10	17
10P LOSS WILD-TYPE	53	60	64	105	40	49

Figure S290. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S291. Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
10P LOSS MUTATED	34	3	26
10P LOSS WILD-TYPE	209	79	83

Figure S291. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S292. Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
10Q LOSS MUTATED	54	1	12	1
10Q LOSS WILD-TYPE	180	152	39	2

Figure S292. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S293. Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
10Q LOSS MUTATED	6	13	1	31	8
10Q LOSS WILD-TYPE	39	97	50	69	79

Figure S293. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S294. Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
10Q LOSS MUTATED	30	5	9	12	8
10Q LOSS WILD-TYPE	64	89	84	70	42

Figure S294. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0057

Table S295. Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
10Q LOSS MUTATED	17	3	29	15
10Q LOSS WILD-TYPE	92	79	106	72

Figure S295. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0076

Table S296. Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
10Q LOSS MUTATED	10	9	13	7	8	20
10Q LOSS WILD-TYPE	51	57	67	104	42	46

Figure S296. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S297. Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
10Q LOSS MUTATED	31	5	31
10Q LOSS WILD-TYPE	212	77	78

Figure S297. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0235 (Fisher's exact test), Q value = 0.051

Table S298. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
10Q LOSS MUTATED	12	4	6	15	11
10Q LOSS WILD-TYPE	91	68	38	47	49

Figure S298. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S299. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
11P LOSS MUTATED	52	5	7	0
11P LOSS WILD-TYPE	182	148	44	3

Figure S299. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00024

Table S300. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
11P LOSS MUTATED	13	12	1	23	7
11P LOSS WILD-TYPE	32	98	50	77	80

Figure S300. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.044

Table S301. Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
11P LOSS MUTATED	30	5	7	8
11P LOSS WILD-TYPE	110	53	71	72

Figure S301. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.028

Table S302. Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
11P LOSS MUTATED	21	5	10	12	7
11P LOSS WILD-TYPE	73	89	83	70	43

Figure S302. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.047

Table S303. Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
11P LOSS MUTATED	18	4	24	9
11P LOSS WILD-TYPE	91	78	111	78

Figure S303. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00694 (Fisher's exact test), Q value = 0.018

Table S304. Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
11P LOSS MUTATED	32	6	25
11P LOSS WILD-TYPE	211	76	84

Figure S304. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0061

Table S305. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
11P LOSS MUTATED	7	5	9	16	10
11P LOSS WILD-TYPE	96	67	35	46	50

Figure S305. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S306. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
11Q LOSS MUTATED	45	4	11	1
11Q LOSS WILD-TYPE	189	149	40	2

Figure S306. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0041

Table S307. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
11Q LOSS MUTATED	13	10	3	21	8
11Q LOSS WILD-TYPE	32	100	48	79	79

Figure S307. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.037

Table S308. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
11Q LOSS MUTATED	11	5	9	15	5
11Q LOSS WILD-TYPE	92	67	35	47	55

Figure S308. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S309. Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
12P LOSS MUTATED	58	2	2	0
12P LOSS WILD-TYPE	176	151	49	3

Figure S309. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S310. Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
12P LOSS MUTATED	9	7	2	32	3
12P LOSS WILD-TYPE	36	103	49	68	84

Figure S310. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S311. Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
12P LOSS MUTATED	30	4	5	13	4
12P LOSS WILD-TYPE	64	90	88	69	46

Figure S311. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00058

Table S312. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
12P LOSS MUTATED	16	3	31	6
12P LOSS WILD-TYPE	93	79	104	81

Figure S312. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0036

Table S313. Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
12P LOSS MUTATED	7	7	9	8	8	21
12P LOSS WILD-TYPE	54	59	71	103	42	45

Figure S313. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S314. Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
12P LOSS MUTATED	23	5	32
12P LOSS WILD-TYPE	220	77	77

Figure S314. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.022

Table S315. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
12P LOSS MUTATED	31	10	8
12P LOSS WILD-TYPE	116	111	65

Figure S315. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S316. Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
12P LOSS MUTATED	10	3	3	22	11
12P LOSS WILD-TYPE	93	69	41	40	49

Figure S316. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S317. Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
12Q LOSS MUTATED	49	1	2	0
12Q LOSS WILD-TYPE	185	152	49	3

Figure S317. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S318. Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
12Q LOSS MUTATED	12	5	1	24	3
12Q LOSS WILD-TYPE	33	105	50	76	84

Figure S318. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S319. Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
12Q LOSS MUTATED	23	3	6	10	4
12Q LOSS WILD-TYPE	71	91	87	72	46

Figure S319. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.0082

Table S320. Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
12Q LOSS MUTATED	17	2	21	6
12Q LOSS WILD-TYPE	92	80	114	81

Figure S320. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S321. Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
12Q LOSS MUTATED	21	4	25
12Q LOSS WILD-TYPE	222	78	84

Figure S321. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0023

Table S322. Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
12Q LOSS MUTATED	11	3	3	18	8
12Q LOSS WILD-TYPE	92	69	41	44	52

Figure S322. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0013

Table S323. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
13Q LOSS MUTATED	29	3	4	1
13Q LOSS WILD-TYPE	205	150	47	2

Figure S323. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S324. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
14Q LOSS MUTATED	101	3	6	1
14Q LOSS WILD-TYPE	133	150	45	2

Figure S324. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S325. Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
14Q LOSS MUTATED	15	21	7	46	11
14Q LOSS WILD-TYPE	30	89	44	54	76

Figure S325. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00054

Table S326. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
14Q LOSS MUTATED	42	17	18	19	9
14Q LOSS WILD-TYPE	52	77	75	63	41

Figure S326. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00129 (Fisher's exact test), Q value = 0.0041

Table S327. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
14Q LOSS MUTATED	30	12	48	15
14Q LOSS WILD-TYPE	79	70	87	72

Figure S327. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0012

Table S328. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
14Q LOSS MUTATED	16	8	19	24	10	31
14Q LOSS WILD-TYPE	45	58	61	87	40	35

Figure S328. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S329. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
14Q LOSS MUTATED	48	14	46
14Q LOSS WILD-TYPE	195	68	63

Figure S329. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.066

Table S330. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
14Q LOSS MUTATED	45	27	11
14Q LOSS WILD-TYPE	102	94	62

Figure S330. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.025

Table S331. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
14Q LOSS MUTATED	25	12	9	26	11
14Q LOSS WILD-TYPE	78	60	35	36	49

Figure S331. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S332. Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
15Q LOSS MUTATED	78	2	10	0
15Q LOSS WILD-TYPE	156	151	41	3

Figure S332. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0011

Table S333. Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
15Q LOSS MUTATED	13	19	6	35	10
15Q LOSS WILD-TYPE	32	91	45	65	77

Figure S333. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.038

Table S334. Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
15Q LOSS MUTATED	5	15	22	9	16
15Q LOSS WILD-TYPE	25	77	60	84	43

Figure S334. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00043

Table S335. Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
15Q LOSS MUTATED	35	8	16	16	10
15Q LOSS WILD-TYPE	59	86	77	66	40

Figure S335. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0034

Table S336. Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
15Q LOSS MUTATED	21	6	39	19
15Q LOSS WILD-TYPE	88	76	96	68

Figure S336. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.089

Table S337. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
15Q LOSS MUTATED	15	8	17	16	11	21
15Q LOSS WILD-TYPE	46	58	63	95	39	45

Figure S337. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00445 (Fisher's exact test), Q value = 0.012

Table S338. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
15Q LOSS MUTATED	43	11	34
15Q LOSS WILD-TYPE	200	71	75

Figure S338. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0031

Table S339. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
15Q LOSS MUTATED	24	5	7	22	11
15Q LOSS WILD-TYPE	79	67	37	40	49

Figure S339. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S340. Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
16P LOSS MUTATED	92	3	4	1
16P LOSS WILD-TYPE	142	150	47	2

Figure S340. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S341. Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
16P LOSS MUTATED	12	20	2	44	12
16P LOSS WILD-TYPE	33	90	49	56	75

Figure S341. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S342. Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
16P LOSS MUTATED	49	10	13	15	7
16P LOSS WILD-TYPE	45	84	80	67	43

Figure S342. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S343. Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
16P LOSS MUTATED	24	8	50	12
16P LOSS WILD-TYPE	85	74	85	75

Figure S343. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S344. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
16P LOSS MUTATED	16	5	14	19	13	32
16P LOSS WILD-TYPE	45	61	66	92	37	34

Figure S344. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S345. Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
16P LOSS MUTATED	42	10	47
16P LOSS WILD-TYPE	201	72	62

Figure S345. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0034

Table S346. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
16P LOSS MUTATED	47	24	8
16P LOSS WILD-TYPE	100	97	65

Figure S346. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S347. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
16P LOSS MUTATED	21	8	2	29	19
16P LOSS WILD-TYPE	82	64	42	33	41

Figure S347. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S348. Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
16Q LOSS MUTATED	101	6	6	1
16Q LOSS WILD-TYPE	133	147	45	2

Figure S348. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S349. Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
16Q LOSS MUTATED	16	15	2	51	18
16Q LOSS WILD-TYPE	29	95	49	49	69

Figure S349. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S350. Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
16Q LOSS MUTATED	50	18	13	19	8
16Q LOSS WILD-TYPE	44	76	80	63	42

Figure S350. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00046

Table S351. Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
16Q LOSS MUTATED	29	15	52	12
16Q LOSS WILD-TYPE	80	67	83	75

Figure S351. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S352. Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
16Q LOSS MUTATED	15	9	14	25	15	34
16Q LOSS WILD-TYPE	46	57	66	86	35	32

Figure S352. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S353. Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
16Q LOSS MUTATED	48	14	50
16Q LOSS WILD-TYPE	195	68	59

Figure S353. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.0071

Table S354. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
16Q LOSS MUTATED	51	29	10
16Q LOSS WILD-TYPE	96	92	63

Figure S354. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S355. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
16Q LOSS MUTATED	20	13	6	30	21
16Q LOSS WILD-TYPE	83	59	38	32	39

Figure S355. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S356. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
17P LOSS MUTATED	145	5	13	1
17P LOSS WILD-TYPE	89	148	38	2

Figure S356. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S357. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
17P LOSS MUTATED	24	38	7	63	16
17P LOSS WILD-TYPE	21	72	44	37	71

Figure S357. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.025

Table S358. Gene #71: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
17P LOSS MUTATED	18	40	25	26	23
17P LOSS WILD-TYPE	12	52	57	67	36

Figure S358. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00311 (Fisher's exact test), Q value = 0.0086

Table S359. Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
17P LOSS MUTATED	65	14	32	21
17P LOSS WILD-TYPE	75	44	46	59

Figure S359. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S360. Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
17P LOSS MUTATED	55	16	27	34	20
17P LOSS WILD-TYPE	39	78	66	48	30

Figure S360. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S361. Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
17P LOSS MUTATED	46	13	62	31
17P LOSS WILD-TYPE	63	69	73	56

Figure S361. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0016

Table S362. Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
17P LOSS MUTATED	23	21	29	26	22	38
17P LOSS WILD-TYPE	38	45	51	85	28	28

Figure S362. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S363. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
17P LOSS MUTATED	82	15	62
17P LOSS WILD-TYPE	161	67	47

Figure S363. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.072

Table S364. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
17P LOSS MUTATED	65	35	26
17P LOSS WILD-TYPE	82	86	47

Figure S364. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00065

Table S365. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
17P LOSS MUTATED	43	13	16	35	19
17P LOSS WILD-TYPE	60	59	28	27	41

Figure S365. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S366. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
17Q LOSS MUTATED	69	0	5	0
17Q LOSS WILD-TYPE	165	153	46	3

Figure S366. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S367. Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
17Q LOSS MUTATED	7	14	0	32	11
17Q LOSS WILD-TYPE	38	96	51	68	76

Figure S367. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00019

Table S368. Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
17Q LOSS MUTATED	30	8	8	11	12
17Q LOSS WILD-TYPE	64	86	85	71	38

Figure S368. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.053

Table S369. Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
17Q LOSS MUTATED	16	6	29	18
17Q LOSS WILD-TYPE	93	76	106	69

Figure S369. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0048

Table S370. Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
17Q LOSS MUTATED	11	9	9	11	9	23
17Q LOSS WILD-TYPE	50	57	71	100	41	43

Figure S370. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S371. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
17Q LOSS MUTATED	30	7	35
17Q LOSS WILD-TYPE	213	75	74

Figure S371. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.064

Table S372. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
17Q LOSS MUTATED	16	7	6	19	9
17Q LOSS WILD-TYPE	87	65	38	43	51

Figure S372. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S373. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
18P LOSS MUTATED	91	13	15	0
18P LOSS WILD-TYPE	143	140	36	3

Figure S373. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.075

Table S374. Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
18P LOSS MUTATED	18	23	18	31	18
18P LOSS WILD-TYPE	27	87	33	69	69

Figure S374. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.073

Table S375. Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
18P LOSS MUTATED	29	19	49	17
18P LOSS WILD-TYPE	80	63	86	70

Figure S375. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S376. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
18Q LOSS MUTATED	119	14	21	0
18Q LOSS WILD-TYPE	115	139	30	3

Figure S376. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00011

Table S377. Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
18Q LOSS MUTATED	25	25	21	46	19
18Q LOSS WILD-TYPE	20	85	30	54	68

Figure S377. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.075

Table S378. Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
18Q LOSS MUTATED	60	15	33	23
18Q LOSS WILD-TYPE	80	43	45	57

Figure S378. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.009

Table S379. Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
18Q LOSS MUTATED	46	22	35	30	13
18Q LOSS WILD-TYPE	48	72	58	52	37

Figure S379. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00071

Table S380. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
18Q LOSS MUTATED	37	19	67	23
18Q LOSS WILD-TYPE	72	63	68	64

Figure S380. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.056

Table S381. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
18Q LOSS MUTATED	25	19	27	32	14	34
18Q LOSS WILD-TYPE	36	47	53	79	36	32

Figure S381. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.004

Table S382. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
18Q LOSS MUTATED	78	20	53
18Q LOSS WILD-TYPE	165	62	56

Figure S382. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.071

Table S383. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
18Q LOSS MUTATED	60	33	20
18Q LOSS WILD-TYPE	87	88	53

Figure S383. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00061

Table S384. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
18Q LOSS MUTATED	32	14	16	35	16
18Q LOSS WILD-TYPE	71	58	28	27	44

Figure S384. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S385. Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
19P LOSS MUTATED	109	0	6	1
19P LOSS WILD-TYPE	125	153	45	2

Figure S385. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S386. Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
19P LOSS MUTATED	8	23	4	63	7
19P LOSS WILD-TYPE	37	87	47	37	80

Figure S386. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.0099

Table S387. Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
19P LOSS MUTATED	49	7	19	16
19P LOSS WILD-TYPE	91	51	59	64

Figure S387. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S388. Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
19P LOSS MUTATED	60	8	14	17	10
19P LOSS WILD-TYPE	34	86	79	65	40

Figure S388. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S389. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
19P LOSS MUTATED	26	5	62	16
19P LOSS WILD-TYPE	83	77	73	71

Figure S389. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S390. Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
19P LOSS MUTATED	15	11	16	14	14	44
19P LOSS WILD-TYPE	46	55	64	97	36	22

Figure S390. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S391. Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
19P LOSS MUTATED	41	9	64
19P LOSS WILD-TYPE	202	73	45

Figure S391. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0032

Table S392. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
19P LOSS MUTATED	52	19	18
19P LOSS WILD-TYPE	95	102	55

Figure S392. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S393. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
19P LOSS MUTATED	16	6	11	37	19
19P LOSS WILD-TYPE	87	66	33	25	41

Figure S393. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S394. Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
19Q LOSS MUTATED	82	0	3	1
19Q LOSS WILD-TYPE	152	153	48	2

Figure S394. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S395. Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
19Q LOSS MUTATED	7	16	1	47	6
19Q LOSS WILD-TYPE	38	94	50	53	81

Figure S395. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S396. Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
19Q LOSS MUTATED	45	5	11	13	7
19Q LOSS WILD-TYPE	49	89	82	69	43

Figure S396. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S397. Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
19Q LOSS MUTATED	23	3	44	11
19Q LOSS WILD-TYPE	86	79	91	76

Figure S397. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S398. Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
19Q LOSS MUTATED	10	10	11	9	12	33
19Q LOSS WILD-TYPE	51	56	69	102	38	33

Figure S398. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S399. Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
19Q LOSS MUTATED	28	7	50
19Q LOSS WILD-TYPE	215	75	59

Figure S399. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00636 (Fisher's exact test), Q value = 0.016

Table S400. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
19Q LOSS MUTATED	38	13	15
19Q LOSS WILD-TYPE	109	108	58

Figure S400. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S401. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
19Q LOSS MUTATED	10	5	7	27	17
19Q LOSS WILD-TYPE	93	67	37	35	43

Figure S401. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.034

Table S402. Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
20P LOSS MUTATED	19	2	1	0
20P LOSS WILD-TYPE	215	151	50	3

Figure S402. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0069

Table S403. Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
20P LOSS MUTATED	8	3	0	6	3
20P LOSS WILD-TYPE	37	107	51	94	84

Figure S403. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.017

Table S404. Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
20P LOSS MUTATED	2	2	3	1	8
20P LOSS WILD-TYPE	28	90	79	92	51

Figure S404. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'RPPA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S405. Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
21Q LOSS MUTATED	144	15	20	2
21Q LOSS WILD-TYPE	90	138	31	1

Figure S405. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #1: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S406. Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
21Q LOSS MUTATED	22	48	7	57	30
21Q LOSS WILD-TYPE	23	62	44	43	57

Figure S406. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0036

Table S407. Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
21Q LOSS MUTATED	54	28	37	36	15
21Q LOSS WILD-TYPE	40	66	56	46	35

Figure S407. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.0086

Table S408. Gene #78: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
21Q LOSS MUTATED	50	23	68	29
21Q LOSS WILD-TYPE	59	59	67	58

Figure S408. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.055

Table S409. Gene #78: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
21Q LOSS MUTATED	26	20	31	39	25	37
21Q LOSS WILD-TYPE	35	46	49	72	25	29

Figure S409. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.002

Table S410. Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
21Q LOSS MUTATED	92	25	61
21Q LOSS WILD-TYPE	151	57	48

Figure S410. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.027

Table S411. Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
21Q LOSS MUTATED	75	44	24
21Q LOSS WILD-TYPE	72	77	49

Figure S411. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.0016

Table S412. Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
21Q LOSS MUTATED	48	22	12	39	22
21Q LOSS WILD-TYPE	55	50	32	23	38

Figure S412. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S413. Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
22Q LOSS MUTATED	132	4	10	0
22Q LOSS WILD-TYPE	102	149	41	3

Figure S413. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S414. Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
22Q LOSS MUTATED	21	31	4	55	22
22Q LOSS WILD-TYPE	24	79	47	45	65

Figure S414. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.0062

Table S415. Gene #79: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
22Q LOSS MUTATED	57	9	27	20
22Q LOSS WILD-TYPE	83	49	51	60

Figure S415. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0059

Table S416. Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
22Q LOSS MUTATED	47	23	25	28	14
22Q LOSS WILD-TYPE	47	71	68	54	36

Figure S416. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 0.019

Table S417. Gene #79: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
22Q LOSS MUTATED	44	18	53	22
22Q LOSS WILD-TYPE	65	64	82	65

Figure S417. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S418. Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
22Q LOSS MUTATED	19	12	22	31	21	38
22Q LOSS WILD-TYPE	42	54	58	80	29	28

Figure S418. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S419. Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
22Q LOSS MUTATED	66	17	60
22Q LOSS WILD-TYPE	177	65	49

Figure S419. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0022

Table S420. Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
22Q LOSS MUTATED	34	14	12	34	21
22Q LOSS WILD-TYPE	69	58	32	28	39

Figure S420. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S421. Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
XP LOSS MUTATED	52	4	5	0
XP LOSS WILD-TYPE	182	149	46	3

Figure S421. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0041

Table S422. Gene #80: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
XP LOSS MUTATED	12	20	2	15	5
XP LOSS WILD-TYPE	33	90	49	85	82

Figure S422. Get High-res Image Gene #80: 'xp loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 5.9e-05

Table S423. Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
XQ LOSS MUTATED	49	3	3	0
XQ LOSS WILD-TYPE	185	150	48	3

Figure S423. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00015

Table S424. Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
XQ LOSS MUTATED	15	16	2	11	3
XQ LOSS WILD-TYPE	30	94	49	89	84

Figure S424. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.092

Table S425. Gene #81: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
XQ LOSS MUTATED	26	5	10	5
XQ LOSS WILD-TYPE	114	53	68	75

Figure S425. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.091

Table S426. Gene #81: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
XQ LOSS MUTATED	36	4	14
XQ LOSS WILD-TYPE	207	78	95

Figure S426. Get High-res Image Gene #81: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/22533931/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/22552605/STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly arm-level cnvs = 81
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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